Permalink warnings after 3.5 upgrade

First of all I spent hours searching all the topics about the WordPress 3.5 upgrade and my specific problem is not listed. Besides that I had multiple problems after the upgrade (not be able to upload media, disappearing buttons in the text editor) so I made sure it wasn’t plugin related.

I deactivated and reactivated all of my plugins, switched to the default Twenty Twelve theme, disabled my functions.php file, cleared my .htaccess, flushed my cache and even manually replaced all the wordpress core files on my server.
But I still get these warnings on the Permalink Settings page:

Warning: is_writable() [function.is-writable]: open_basedir restriction in effect. File(/) is not within the allowed path(s): (/home/username/:/tmp:/var/tmp:/usr/local/lib/php/) in /home/username/domains/domain-a.com/public_html/blog/wp-admin/options-permalink.php on line 131

Warning: is_writable() [function.is-writable]: open_basedir restriction in effect. File(/) is not within the allowed path(s): (/home/username/:/tmp:/var/tmp:/usr/local/lib/php/) in /home/username/domains/domain-a.com/public_html/blog/wp-admin/includes/misc.php on line 133

Besides that, it says my .htaccess is not writable, even when I change the permissions to 777. My site is fully functional by the way, but I would like to find out where these warnings come from.

Yes I have (regarding a different open_basedir error) but they say it has nothing to do with their configurations and that there’s some PHP script within WordPress that is trying to call the file or folder ‘/’. Besides that, nothing has changed on their side since the upgrade to WordPress 3.5.

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